p53 deficiency mediates cisplatin resistance by upregulating RRM2 and crotonylation of RRM2K283 through the downregulation of SIRT7.

p53 deficiency plays a crucial role in chemotherapy resistance through various biological events, including posttranslational modifications (PTMs). Recently, lysine crotonylation (Kcr) has been shown to play a vital role in cancer progression. However, the global p53-regulated crotonylome and the function of these altered Kcr proteins after p53 deficiency remain unclear. In this study, we used a SILAC-based quantitative crotonylome to identify 3,520 Kcr in 1924 crotonylated proteins in response to p53 knockout. We found that increased crotonylation of RRM2 at K283 (RRM2K283Cr) in the presence of p53 deficiency promoted HCT116 cell resistance to cisplatin. We discovered that SIRT7 could be the decrotonylase of RRM2 and was downregulated after p53 knockout, resulting in increased RRM2K283Cr. Mechanistically, p53 deficiency inhibited cell apoptosis by upregulating RRM2 protein expression and RRM2K283Cr-mediated cleaved-PARP1 and cleaved-caspase3 expression, and SIRT7 was downregulated to upregulate crotonylation of RRM2 upon p53 deficiency. In conclusion, our results indicated that p53 deficiency plays a malignant role in colon cancer resistance to cisplatin therapy by regulating RRM2 protein and RRM2K283Cr expression. Our findings provide a novel therapeutic target against p53-deficient cancer.

Association between ambient particulate matter exposure and mitochondrial DNA copy number: A systematic review and meta-analysis.

BACKGROUND: Ambient particulate matter (PM) has been recognized as inducing oxidative stress, which could contribute to mitochondrial damage and dysfunction. However, studies investigating the association between ambient PM and mitochondria, particularly mitochondrial DNA copy number (mtDNA-CN), have yielded inconsistent results. METHODS: We conducted comprehensive literature searches to identify observational studies published before July 17, 2023, examining the association between ambient PM exposure and mtDNA-CN. Meta-analysis using random effects model was employed to calculate the pooled effect estimates for general individual exposures, as well as for prenatal exposure with specific trimester. Additionally, the quality and level of evidence for each exposure-outcome pair was evaluated. RESULTS: A total of 10 studies were included in the systematic review and meta-analysis. The results indicated that general individual exposure to PM2.5 (ß = -0.084, 95 % CI: -0.521, 0.353; I2 = 93 %) and PM10 (ß = 0.035, 95 % CI: -0.129, 0.199; I2 = 95 %) did not significantly affect mtDNA-CN. Prenatal exposure to PM2.5 (ß = 0.023, 95 % CI: -0.087, 0.133; I2 = 0 %) and PM10 (ß = 0.006, 95 % CI: -0.135; 0.147; I2 = 51 %) were also not significantly associated with mtDNA-CN in offspring. The level of evidence for each tested exposure-outcome pair was assessed as "inadequate." CONCLUSIONS: The findings of this systematic review and meta-analysis indicate that there is an "inadequate" strength of evidence for the association between general individual or prenatal exposure to ambient PM and mtDNA-CN. Future research necessitates studies with more rigorous design, enhanced control of confounding factors, and improved measures of exposure to substantiate our findings.

LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data.

MOTIVATION: From a systematic perspective, it is crucial to infer and analyze gene regulatory network (GRN) from high-throughput single-cell RNA sequencing data. However, most existing GRN inference methods mainly focus on the network topology, only few of them consider how to explicitly describe the updated logic rules of regulation in GRNs to obtain their dynamics. Moreover, some inference methods also fail to deal with the over-fitting problem caused by the noise in time series data. RESULTS: In this article, we propose a novel embedded Boolean threshold network method called LogBTF, which effectively infers GRN by integrating regularized logistic regression and Boolean threshold function. First, the continuous gene expression values are converted into Boolean values and the elastic net regression model is adopted to fit the binarized time series data. Then, the estimated regression coefficients are applied to represent the unknown Boolean threshold function of the candidate Boolean threshold network as the dynamical equations. To overcome the multi-collinearity and over-fitting problems, a new and effective approach is designed to optimize the network topology by adding a perturbation design matrix to the input data and thereafter setting sufficiently small elements of the output coefficient vector to zeros. In addition, the cross-validation procedure is implemented into the Boolean threshold network model framework to strengthen the inference capability. Finally, extensive experiments on one simulated Boolean value dataset, dozens of simulation datasets, and three real single-cell RNA sequencing datasets demonstrate that the LogBTF method can infer GRNs from time series data more accurately than some other alternative methods for GRN inference. AVAILABILITY AND IMPLEMENTATION: The source data and code are available at https://github.com/zpliulab/LogBTF.

PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression.

During breast cancer metastasis, the developmental process epithelial-mesenchymal (EM) transition is abnormally activated. Transcriptional regulatory networks controlling EM transition are well-studied; however, alternative RNA splicing also plays a critical regulatory role during this process. Alternative splicing was proved to control the EM transition process, and RNA-binding proteins were determined to regulate alternative splicing. A comprehensive understanding of alternative splicing and the RNA-binding proteins that regulate it during EM transition and their dynamic impact on breast cancer remains largely unknown. To accurately study the dynamic regulatory relationships, time-series data of the EM transition process are essential. However, only cross-sectional data of epithelial and mesenchymal specimens are available. Therefore, we developed a pseudotemporal causality-based Bayesian (PCB) approach to infer the dynamic regulatory relationships between alternative splicing events and RNA-binding proteins. Our study sheds light on facilitating the regulatory network-based approach to identify key RNA-binding proteins or target alternative splicing events for the diagnosis or treatment of cancers. The data and code for PCB are available at: http://hkumath.hku.hk/~wkc/PCB(data+code).zip.

Contrasting response of fungal versus bacterial residue accumulation within soil aggregates to long-term fertilization.

Soil microorganisms are critical for soil carbon (C) cycling. They primarily regulate the turnover of the soil organic C (SOC) by adjusting their community structure, and contributing residues with a considerable amount to the resistant SOC. Nevertheless, how long-term fertilization (e.g., the combination of manure and chemical fertilizer) affects the spatial distribution of both living microbial communities and dead microbial residue within soil aggregate fractions remains largely unclear. In this study, we analyzed changes in microbial community (lipid biomarkers) and microbial residue retention (amino sugar biomarkers), and also calculated the contribution of microbial residue to organic C in bulk soil and different soil aggregates (> 2 mm, 1-2 mm, 0.25-1 mm, and < 0.25 mm) in Alfisols treated with 29 years fertilization or no fertilization (control). Our results showed that long-term fertilization significantly increased the mean weight diameter (MWD) of aggregates and organic C contents in all aggregate fractions. The fertilization treatment increased the contents of PLFAs and microbial residue C, but the relative contribution of microbial residue to SOC was higher in the control (56.8% vs. 49.0%), due to the low SOC background caused by much lower level of non-microbially derived C input. These results suggested that long-term fertilization could increase SOC by accumulating both plant- and microbial-derived C, while the C deficient soil is more dependent on the accumulation of microbial residues. Long-term fertilization promoted the enrichment of bacterial-derived muramic acid in micro aggregates, but increased the proportion of fungal-derived glucosamine in macro aggregates. Meanwhile, the contribution of bacterial residue to organic C in the fertilization treatment was higher in micro aggregates (7.6% for > 2 mm vs. 9.2% for < 0.25 mm aggregate), while the contribution of fungal residue was higher in macro aggregate fractions (40.9% for > 2 mm vs. 35.7% for < 0.25 mm aggregate). The above results indicated that long-term fertilization could drive the differentiation of heterogeneous microbial residue accumulation patterns that significantly alter the contribution of fungal- versus bacterial-derived C to organic C within soil aggregate fractions.

miR-9-5p promotes myogenic differentiation via the Dlx3/Myf5 axis.

MicroRNAs play an important role in myogenic differentiation, they bind to target genes and regulate muscle formation. We previously found that miR-9-5p, which is related to bone formation, was increased over time during the process of myogenic differentiation. However, the mechanism by which miR-9-5p regulates myogenic differentiation remains largely unknown. In the present study, we first examined myotube formation and miR-9-5p, myogenesis-related genes including Dlx3, Myod1, Mef2c, Desmin, MyoG and Myf5 expression under myogenic induction. Then, we detected the expression of myogenic transcription factors after overexpression or knockdown of miR-9-5p or Dlx3 in the mouse premyoblast cell line C2C12 by qPCR, western blot and myotube formation under myogenic induction. A luciferase assay was performed to confirm the regulatory relationships between not only miR-9-5p and Dlx3 but also Dlx3 and its downstream gene, Myf5, which is an essential transcription factor of myogenic differentiation. The results showed that miR-9-5p promoted myogenic differentiation by increasing myogenic transcription factor expression and promoting myotube formation, but Dlx3 exerted the opposite effect. Moreover, the luciferase assay showed that miR-9-5p bound to the 3'UTR of Dlx3 and downregulated Dlx3 expression. Dlx3 in turn suppressed Myf5 expression by binding to the Myf5 promoter, ultimately inhibiting the process of myogenic differentiation. In conclusion, the miR-9-5p/Dlx3/Myf5 axis is a novel pathway for the regulation of myogenic differentiation, and can be a potential target to treat the diseases related to muscle dysfunction.

Low doses of niclosamide and quinacrine combination yields synergistic effect in melanoma via activating autophagy-mediated p53-dependent apoptosis.

Malignant melanoma is a highly aggressive, malignant, and drug-resistant tumor. It lacks an efficient treatment approach. In this study, we developed a novel anti-melanoma strategy by using anti-tapeworm drug niclosamide and anti-malarial drug quinacrine, and investigated the molecular mechanism by in vitro and in vivo assays. Meanwhile, other types of tumor cells, immortalized epithelial cells and bone marrow mesenchymal stem cells were used to evaluate the universal role of anti-cancer and safety of the strategy. The results showed, briefly, an exposure to niclosamide and quinacrine led to an increased apoptosis-related protein p53, cleaved caspase-3 and cleaved PARP and autophagy-related protein LC3B expression, and a decreased expression of autophagy-related protein p62, finally leading to cell apoptosis and autophage. After inhibiting autophagy by Baf-A1, flow cytometry and western blot showed that the expression of apoptosis-related proteins was down-regulated and the number of apoptotic cells decreased. Subsequently, in the siRNA-mediated p53 knockdown cells, the expression of apoptosis-related proteins and the number of apoptotic cells were also reduced, while the expression of autophagy-related proteins including LC3B, p62 did not change significantly. To sum up, we developed a new, safe strategy for melanoma treatment by using low doses of niclosamide and quinacrine to treat melanoma; and found a novel mechanism by which the combination application of low doses of niclosamide and quinacrine exerts an efficient anti-melanoma effect through activation of autophagy-mediated p53-dependent apoptosis. The novel strategy was verified to exert a universal anti-cancer role in other types of cancer.

Streptococcus mutans-associated bacteria in dental plaque of severe early childhood caries.

BACKGROUND: Streptococcus mutans (S. mutans) is a potential pathogenic bacteria of dental caries. However, the level of S. mutans is low in some children with severe early childhood caries (SECC). AIM: To evaluate the effect of S. mutans level on dental microbiome and cariogenesis. METHODS: The oral microbiota was compared between caries-free group (CF) and SECC group.16S rRNA gene sequencing was used for S. mutans level bacterial community analysis. The candidate bacteria that were closely related with S. mutans abundance were identified and confirmed by absolute quantitative real-time PCR in clinical dental plaque samples from CF and SECC groups. RESULTS: Through in-depth analysis of dental plaque microorganism, Leptotrichia, Selenomonas and Prevotella_7 were found in the S. mutans-low group (p < 0.05) and Porphyromonas, Selenomonas_3 were found in the S. mutans-high group (p < 0.05). Through quantitative real-time PCR, Leptotrichia, Selenomonas and Prevotella_7 were identified as the potential biomarkers of SECC when S. mutans was at a low level. CONCLUSION: Leptotrichia, Selenomonas and Prevotella_7 are identified as potential biomarkers in SECC with a low abundance or without S. mutans. Our study may shed light on the understanding of caries occurrence in SECC with low abundance of S. mutans. ABBREVIATIONS: S. mutans, Streptococcus mutans; CF, caries-free; SECC, severe early childhood caries; ECC, early childhood caries; rRNA, ribosome RNA; qPCR, Quantitative real-time PCR; OTUs, operational taxonomic units; ANOVA, analysis of variance; LDA, Linear discriminant analysis; LEfSe, Linear discriminant analysis effect size; COG, Groups of proteins; NMDS, Non-MetricMulti-Dimensional Scaling; IL-1ß, interleukin -1ß; IL-6, interleukin-6; IL-8, interleukin-8; IL-10, interleukin-10.

Astragaloside IV suppresses migration and invasion of TGF-ß1-induced human hepatoma HuH-7 cells by regulating Nrf2/HO-1 and TGF-ß1/Smad3 pathways.

Astragaloside IV (AS-IV), one of the major compounds extract from Astragalus membranaceus, has shown attractive anti-cancer effects in certain malignancies. Oxidative stress (OS) is considered as a crucial factor in promoting the progression of hepatocellular carcinoma (HCC). In response to OS, nuclear factor erythroid 2-related factor 2 (Nrf2) upregulates and induces heme oxygenase 1 (HO-1) to combat oxidative damages. The phosphorylation of the COOH-terminal of Smad3 (pSmad3C) activates p21 to resist HCC progression, while the phosphorylation of the linker region of Smad3 (pSmad3L) up-regulates c-Myc transcription to exert promoting effect towards HCC. This study aimed to explore whether AS-IV suppresses migration and invasion of human hepatoma HuH-7 cells by regulating Nrf2/HO-1 and TGF-ß1/Smad3 pathways. HuH-7 cells were induced with TGF-ß1 (9 or 40 pM) to establish HCC model in vitro and pretreated with AS-IV at different concentration (5, 10, and 20 µM) for 24 h. Cell proliferation, migration, invasion, and intracellular reactive oxygen species (ROS) of HuH-7 cells were measured. The expression of Nrf2, pSmad3C, Nrf2/pNrf2, HO-1, pSmad3C/3L, c-Myc, and p21 were detected. Exposure of HuH-7 cells to TGF-ß1 enhanced the cell proliferation, migration, invasion, and ROS production. Pretreatment with AS-IV (5, 10, and 20 µM) significantly reduced the cell proliferation, migration, invasion, and ROS production in HuH-7 cells. Furthermore, AS-IV increased the expressions of Nrf2/pNrf2, HO-1, pSmad3C, and p21, meanwhile reduced the expressions of pSmad3L and c-Myc. In conclusion, our study suggested that AS-IV inhibit HuH-7 cells migration and invasion, which related to activate Nrf2/HO-1 pathway, up-regulation pSmad3C/p21 pathway, and down-regulation pSmad3L/c-Myc pathway. The present research supports the notion that AS-IV may be a latent agent for the treatment of HCC.

Deficient or R273H and R248W Mutations of p53 Promote Chemoresistance to 5-FU via TCF21/CD44 Axis-Mediated Enhanced Stemness in Colorectal Carcinoma.

Background: p53 mutations are highly frequent in various human cancers and are reported to contribute to tumor malignance and chemoresistance. In this study, we explored the mechanism by which mutant p53 promotes carcinogenesis and chemoresistance and provided novel insights into cancer therapy. Materials and methods: A total of 409 patients with colorectal carcinoma from TCGA database were subdivided into two groups according to the p53 status, namely, mutant p53 and wild-type p53, following with GSEA analysis. The differences of the clinicopathologic index were also analyzed. Two HCT116 cell lines containing hot spots at codons R273H and R248W of p53 were constructed based on HCT116 with knockout p53, respectively. Cell viability, mobility, clonogenesis, and stemness were detected by CCK8, transwell migration and invasion, colonogenic, and sphere formation assays. Resistance to 5-FU was examined by live-dead staining and flow cytometry. qPCR, Western blot, and luciferase reporter assay were performed to identify that deficient or mutant p53 promoted chemoresistance of the colorectal carcinoma cell line HCT116 through the TCF21/CD44 signaling pathway, with the following rescue assays by overexpression of TCF21 and knockdown of CD44. Results: Patients with recurrence harbor a higher frequency of mutant p53 than those without recurrence (p < 0.05). The mutant p53 group developed a larger tumor than the wild-type one. GSEA analysis showed that oncogenic signatures were enriched in the mutant p53 group. Extracellular assays showed that cancer cells with deficient or mutant p53 (R273H and R248W, respectively) promoted colon cancer cell growth, migration, invasion, and stemness. The mutant cancer cells were also observed to be significantly resistant to 5-FU. Xenografts also confirmed that HCT116 cells harboring deficient or mutant p53 promoted cancer growth and 5-FU tolerance. Luciferase reporter assay showed that deficient or mutant p53 R237H and R248W endowed cancer cells with chemoresistance by activating CD44 via repressing the nuclear transcription factor TCF21 expression. Overexpression of TCF21 or knockdown of CD44 could rescue the sensitivity to 5-FU in deficient and mutant p53 HCT116 cell lines. Conclusion: Our results, for the first time, reveal a novel deficient or mutant p53/TCF21/CD44 signaling pathway which promotes chemoresistance in colorectal carcinoma. The axis could be an effective therapeutic strategy against deficient- or mutant p53-driven chemoresistance.

Variable structure controller design for Boolean networks.

The paper investigates the variable structure control for stabilization of Boolean networks (BNs). The design of variable structure control consists of two steps: determine a switching condition and determine a control law. We first provide a method to choose states from the reaching mode. Using this method, we can guarantee that the number of nodes which should be controlled is minimized. According to the selected states, we determine the switching condition to guarantee that the time of global stabilization in the BN is the shortest. A control law is then determined to ensure that all selected states can enter into the sliding mode, such that any initial state can arrive in the steady-state mode. Some examples are provided to illustrate the theoretical results.

Sampled-Data State Feedback Stabilization of Boolean Control Networks.

In this letter, we investigate the sampled-data state feedback control (SDSFC) problem of Boolean control networks (BCNs). Some necessary and sufficient conditions are obtained for the global stabilization of BCNs by SDSFC. Different from conventional state feedback controls, new phenomena observed the study of SDSFC. Based on the controllability matrix, we derive some necessary and sufficient conditions under which the trajectories of BCNs can be stabilized to a fixed point by piecewise constant control (PCC). It is proved that the global stabilization of BCNs under SDSFC is equivalent to that by PCC. Moreover, algorithms are given to construct the sampled-data state feedback controllers. Numerical examples are given to illustrate the efficiency of the obtained results.

Feedback Controller Design for the Synchronization of Boolean Control Networks.

This brief investigates the partial and complete synchronization of two Boolean control networks (BCNs). Necessary and sufficient conditions for partial and complete synchronization are established by the algebraic representations of logical dynamics. An algorithm is obtained to construct the feedback controller that guarantees the synchronization of master and slave BCNs. Two biological examples are provided to illustrate the effectiveness of the obtained results.

[Reponses of soil total organic carbon and dissolved organic carbon to simulated nitrogen deposition in temperate typical steppe in Inner Mongolia, China].

Based on a field manipulative nitrogen (N) addition experiment, the effects of atmospheric N deposition level change on the contents, inter-annual variation and profile distribution of soil total organic carbon (TOC) and dissolved organic carbon (DOC) were investigated from May, 2008 to October, 2011 in a temperate typical steppe in Inner Mongolia of China, and the relationship between TOC and DOC was also discussed. The treatments in the manipulative experiment included N additions at rates of 0, 5, 10, and 20 g x (m2 x a)(-1), representing the control (CK), low N (LN), medium N (MN), and high N (HN) treatment, respectively. The results indicated that the concentrations of soil TOC and DOC decreased progressively with soil depth in all cases except for the DOC at 10-20 cm depth in individual years. The increase of N input in typical steppe did not change the vertical distribution of soil TOC and DOC, but reduced the vertical variation of TOC and increased the vertical variation of DOC in the surface soil horizon. In addition, the contents of soil TOC and DOC at 0- 10 cm and 10- 20 cm soil layers changed insignificantly after the continuous increase in anthropogenic N input for four years. The soil organic C density of 0-20 cm soil layer for different N treatment levels varied between 3.9 kg x m(-2) and 5.6 kg x m(-2), and the soil organic C densities of fertilized treatments in the first two years were similar to or slightly lower than those of CK, while in the following two years, the increase in N deposition gradually played a positive role in increasing soil organic C density, but the differences in soil TOC and DOC contents between CK and fertilized plots were not significant (P > 0.05). The ratio of soil DOC to TOC (DOC/TOC) varied from 0.32% to 1.09%. The increase in N deposition generally lowered the proportion of DOC in soil TOC, which was conducive to the accumulation of soil organic C. The change of soil DOC was positively correlated with that of TOC (P < 0.01). The temporal variations of soil DOC in different N treatments were all far greater than those of TOC, and the soil DOC was the important sensitive indicator for predicting and evaluating the response of soil C pool to the change in atmospheric N deposition in the temperate grassland ecosystem.

Differential responses of short-term soil respiration dynamics to the experimental addition of nitrogen and water in the temperate semi-arid steppe of Inner Mongolia, China.

We examined the effects of simulated rainfall and increasing N supply of different levels on CO2 pulse emission from typical Inner Mongolian steppe soil using the static opaque chamber technique, respectively in a dry June and a rainy August. The treatments included NH4NO3 additions at rates of 0, 5, 10, and 20 g N/(m(2)·year) with or without water. Immediately after the experimental simulated rainfall events, the CO2 effluxes in the watering plots without N addition (WCK) increased greatly and reached the maximum value at 2 hr. However, the efflux level reverted to the background level within 48 hr. The cumulative CO2 effluxes in the soil rang ed from 5.60 to 6.49 g C/m(2) over 48 hr after a single water application, thus showing an increase of approximately 148.64% and 48.36% in the effluxes during both observation periods. By contrast, the addition of different N levels without water addition did not result in a significant change in soil respiration in the short term. Two-way ANOVA showed that the effects of the interaction between water and N addition were insignificant in short-term soil CO2 effluxes in the soil. The cumulative soil CO2 fluxes of different treatments over 48 hr accounted for approximately 5.34% to 6.91% and 2.36% to 2.93% of annual C emission in both experimental periods. These results stress the need for improving the sampling frequency after rainfall in future studies to ensure more accurate evaluation of the grassland C emission contribution.

[Microbial response mechanism for drying and rewetting effect on soil respiration in grassland ecosystem: a review].

As one of the most important and wide distribution community type among terrestrial ecosystems, grassland ecosystem plays a critical role in the global carbon cycles and climate regulation. China has extremely rich grassland resources, which have a huge carbon sequestration potential and are an important part of the global carbon cycle. Drying and rewetting is a common natural phenomenon in soil, which might accelerate soil carbon mineralization process, increase soil respiration and exert profound influence on microbial activity and community structure. Under the background of the global change, the changes in rainfall capacity, strength and frequency would inevitably affect soil drying and wetting cycles, and thus change the microbial activity and community structure as well as soil respiration, and then exert important influence on global carbon budget. In this paper, related references in recent ten years were reviewed. The source of soil released, the trend of soil respiration over time and the relationship between soil respiration and microbial biomass, microbial activity and microbial community structure during the processes of dry-rewetting cycle were analyzed and summarized, in order to better understand the microbial response mechanism for drying and rewetting effecting on soil respiration in grassland ecosystem, and provide a certain theoretical basis for more accurate evaluation and prediction of future global carbon balance of terrestrial ecosystems and climate change.